Objective To investigate the clinical features, prognosis, and factors associated with influenza-associated encephalopathy (IAE) in children. Methods Clinical data of 186 children hospitalized with influenza and neurological symptoms at the Children's Hospital of Chongqing Medical University from January 2015 to December 2025 were retrospectively analyzed. Based on whether they met the diagnostic criteria for acute encephalopathy, patients were divided into the IAE group and the non-IAE group. Clinical manifestations, laboratory findings, neuroimaging characteristics, treatment, and outcomes were compared between the two groups. Results The IAE group included 58 patients (31.2%), with seizures and persistent disturbance of consciousness as the main neurological manifestations (40 cases each, 69.0%). Compared with the non-IAE group, the IAE group had an older age at onset and higher rates of electroencephalographic and neuroimaging abnormalities (P<0.05), with significantly more frequent involvement of deep brain structures including the thalamus, basal ganglia, and brainstem (P<0.001). In the IAE group, 7 patients (12.1%) died during hospitalization, and 12(20.7%) had neurological sequelae at discharge. At a median follow-up of 12 months, the incidences of motor, language, and cognitive dysfunctions, as well as the rate of poor long-term prognosis, were significantly higher in the IAE group (P<0.05). Multivariable logistic regression analysis showed that older age (OR=1.19) and elevated serum lactate dehydrogenase (OR=1.01) were positively associated with the occurrence of IAE (both P<0.05). Conclusions Pediatric IAE is characterized by seizures and persistent disturbance of consciousness, with a predilection for deep brain structures and a high risk of poor prognosis. Older age and elevated serum lactate dehydrogenase are closely associated with the development of IAE.